Scanning & Image Processing
For digitizing histology slides, we purchased a Scanscope T2 scanner from Aperio Technologies, Inc. This system allows us to scan at both 20x and 40x magnification. We can scan entire slides or sections of slides and can scan up to 120 slides in a batch mode with the T2's robotic device.
While high-throughput can be achieved with batch scanning, production scans have been scanned individually to give us finer control over the placement of focus points. This time-consuming process is required to obtain the detail necessary for high-quality images.
Resulting images are pyramidal SVS files. This means that aside from the original, full-sized image, reduced sized copies are also stored in the same file, allowing special software to view these images as virtual slides with greater efficiency.
Images captured by the scanner have been adjusted to maximize ease of interpretation of the atlas. The digital processing minimizes artifacts introduced during specimen preparation and photography. Artifacts addressed include color balance, cloudiness introduced by spherical aberration, and the separation of relevant foreground data contained in the tissue from distracting background artifact.
